Bayesian analysis of semiparametric linear-circular models

In many environmental and agricultural studies, data are collected on both linear and circular random variables, with possible dependence between the variables. Classically, the analysis of such data has been carried out in a classical regression framework. We propose a Bayesian hierarchical framework to handle all forms of uncertainty arising in a linear-circular data set. One novelty of our multivariate linear-circular model is that, marginally, the circular component is assumed to be a mixture model with an unknown number of von Mises (or circular normal) distributions. We use the Dirichlet process to introduce variability in the model dimensionality, and develop a simple Gibbs sampling algorithm for simulating the mixture components. Although we illustrate our methodology on von Mises mixtures, it is widely applicable. We thus avoid complicated reversible-jump Markov chain Monte Carlo methods, which are considered ideal for analyzing mixtures of unknown number of distributions. We illustrate our methodologies with simulated and real data sets. Using pseudo-Bayes factors, we also compare different models associated with both fixed and variable numbers of von Mises distributions. Our findings suggest that models associated with varying numbers of mixture components perform at least as well as those with known numbers of mixture components. We tentatively argue that model averaging associated with variable number of mixture components improves the model’s predictive power, which compensates for the lack of knowledge of the actual number of mixture components.     

Efficiency of uterine fluid cytology in the diagnosis of subclinical endometritis in the water buffalo (Bubalus bubalis)

This study compared endometrial cytology vis‐a‐vis uterine fluid cytology for assessment of uterine health in clinically normal and subclinical endometritis (SE)‐affected buffaloes. Uterine fluid samples and endometrial samples were collected from the buffaloes (n = 38) at oestrus using blue sheath and cytobrush, respectively. The smears were stained with Field stain for 3 minutes, and a minimum of 400 cells were counted in each smear for determination of the percentage of polymorphonuclear (PMN) leucocyte. The incidence of subclinical endometritis, based on the cytobrush cytology, was 23.08%. The correlation between cytobrush cytology with uterine fluid cytology was positive and significant (r = .37; p = .02). The ratio of PMN leucocyte in cytobrush cytology to uterine fluid cytology was 1:2.4. ROC analysis revealed that the threshold value of 6.16% PMN leucocyte in uterine fluid cytology showed a diagnostic sensitivity and specificity of 100% in differentiating normal from SE‐affected buffaloes. In conclusion, collection of uterine fluid was easier compared to collection of endometrial samples using cytobrush and the percentage of PMN leucocyte in uterine fluid cytology can be used as a tool for diagnosis of subclinical endometritis in buffaloes.     

Antisperm antibodies in repeat‐breeding cows: Frequency,detection and validation of threshold levels employing sperm immobilization,sperm agglutination and immunoperoxidase assay

Antisperm antibodies have been found in repeat‐breeding(RB) cows, and those causing agglutination and/or immobilization of sperm are considered to be closely related to unexplained infertility. However, a standard protocol for identifying antisperm antibodies (ASA) in cattle is not validated. Therefore, an investigation was undertaken to evaluate sperm immobilization (SIT), sperm agglutination (SAT) and immunoperoxidase (IPT)assays for detection of ASA in serum and their respective threshold levels for confirmation. Animals (heifers, normally breeding, repeat‐breeding and pregnant animals) that were free from IBR, brucellosis and uterine infections (screened by clinical examination) were included in the study. Sperm agglutinating, sperm immobilizing and antisperm antibodies evaluated by respective assay were significantly higher (p < .05) in RB cows compared to other groups. The SIT assay was able to identify 61% of RB caused by ASA, more than those employing SAT and IPT. Furthermore, a dilution rate of 1:5 and 1:80 (confirms 59.0 and 57.0% RB+ve)were sufficient to diagnose ASA by SAT and IPT, respectively. Results indicate the presence of __12.6% clumped spermatozoa and __ 2.6%(cut‐off value) peroxidase‐positive spermatozoa at 1:5 and 1:80 dilutions diagnosed with SAT and IPT, respectively, may be considered as repeaters arising out of ASA. Furthermore, study also showed the presence of lower incidence of ASA positivity in other groups of animals (heifer<normal breeder<pregnant animals) compared to repeaters. Study results show that although IPT is more specific and accurate but SAT and SIT are comparatively simple and cost‐effective assays suitable for detecting ASA under field conditions and thus can be recommended for screening of repeaters.     

Characterization of shiga toxin producing (STEC) and enteropathogenic Escherichia coli (EPEC) in raw yak (Poephagus grunniens) milk and milk products

Thirty-one shiga toxin-producing (STEC) and 6 enteropathogenic Escherichia coli (EPEC) were isolated from 87 raw yak milk and 63 'churpi' samples. Of 18 stx(1) positive isolates (48.6%), 14 carried stx(1c) (77.7%). Subtyping of 28 stx(2) positive isolates (75.7%) revealed the presence of stx(2c) (9, 32.1%), stx(2d) (3, 10.7%), stx(2e) (1, 3.57%) and stx(2f) (3, 10.7%) variants. Furthermore, intimin (eaeA), enterohaemolysin (ehxA), autoagglutinating adhesin (saa), iha (adherence conferring protein), efa1 (EHEC factor for adherence), bundle forming pilli (bfpA) and toxB (type III secreted protein encoded on LEE Island, similar to toxin B of Clostridium difficile) genes were detected in 14, 16, 12, 4, 3, 2 and 2 isolates, respectively. Univariate and multivariate analysis depicted that both stx(1) and stx(2) or their variants were more likely to occur in isolates from Arunachal Pradesh (p<0.04) rather than Sikkim. Dendogram constructed on the basis of RAPD and ERIC PCR profile distributed the STEC and EPEC isolates in separate clusters irrespective of their sources and serotypes. The STEC and EPEC isolates exhibited resistance against erythromycin, amikacin, azithromycin, amoxicillin, ampicillin+cloxacillin, cephalothin, furazolidone, gentamicin, kanamycin, streptomycin and tetracycline. This is the first ever report on occurrence and characterization of STEC and EPEC isolated from yak milk and milk products.     

Polymorphisms in GnRHI and GnRHII genes and their association with egg production and egg quality traits in chicken

1. Two candidate genes, namely, Gonadotropin releasing hormone I (GnRHI) and Gonadotropin releasing hormone II (GnRHII) play pivotal roles in ovulation and egg production in chicken. The objective of this study was to explore polymorphism in these genes and to estimate the effects of polymorphism of these two genes on egg production and egg quality traits in White Leghorn laying hens.

2. Single strand conformation polymorphism followed by sequencing was performed to detect polymorphism in these genes.

3. The coding regions of the GnRHI and GnRHII genes were found to be polymorphic. In the GnRH1 gene, 12 haplotypes were determined, of which the h1 haplotype was predominant and the h5, h9 and h11 haplotypes were the least frequent ones. In the GnRHII gene, eight haplotypes were found, of which the h1 haplotype was the most frequent and the h6 was the least frequent haplotype in the White Leghorn population.

4. The haplogroups of GnRHI had a significant effect on body weight and egg production up to 64 weeks of age, yolk content, Haugh units and egg shell parameters. The h1h2 haplogroup of the GnRHI gene showed the highest egg production, with 211.0 ± 24.3 eggs up to 64 weeks of age, while the highest yolk content and Haugh unit was found in h3h10 haplogrouped birds. The haplogroups of GnRHII had a significant effect on age at sexual maturity (ASM) where the shortest ASM was found in the h1h4 birds (147.3 ± 5.9 d) and the longest ASM was observed in the h1h3 birds (160.6 ± 23.4 d).

5. It was concluded that GnRHI and GnRHII genes are polymorphic and have a significant effect on body weight, egg production and egg quality traits in White Leghorn laying hens.     

Plasma growth hormone concentrations in female yak (Poephagus grunniens L.) of different ages:Relations with age and body weight

The role of growth hormone (GH) in postnatal growth is well established. Its basal level and relation to growth performance in different age group yaks has not been characterized until now. To estimate the normal blood GH level in yaks, a total of eighty five female yaks were divided in to thirteen age groups. BW of all animals was recorded on two consecutive days per week and average of weekly BW was considered for growth rate calculation. Blood samples collected twice weekly for four consecutive weeks were assayed for GH by a direct, simple and highly sensitive enzyme immunoassay (EIA) on microtitre plates using the biotin–streptavidin amplification system and the second antibody coating technique developed for the first time in this species. The EIA was carried out directly in 100 μL of yak plasma. The sensitivity of EIA procedure was 20 pg/well GH, which corresponds to 0.2 ng/mL plasma For the biological validation of assay, 2 mature yaks were administered (10 μg, iv) with a synthetic analogue of GHRH and blood samples were collected at 15-min interval using indwelling jugular catheter beginning 2 h prior to GHRH injection till 8 h thereafter. In both the animals, sharp increases in GH concentrations were recorded 75 min post GHRH administration, which confirms the biological validation of the EIA. It was found that mean GH among the age groups differ (p < 0.05). With increasing age and BW, GH level decreased. The age groups with higher plasma GH showed higher growth rates (r = 0.73). In conclusion, a highly sensitive enzymeimmunoassay procedure has been developed for the first time to determine plasma GH levels in bovine (yak) plasma. A close relationship of plasma GH concentration with age, BW and growth rates was found in yaks.     

Genotypic characterisation of Indian cattle, buffalo and sheep isolates of Echinococcus granulosus

Twelve isolates of Echinococcus granulosus, collected from domestic animals, including cattle, buffalo and sheep were analysed for DNA nucleotide sequence variation within mitochondrial cytochrome c oxidase I (coxI), NADH dehydrogenase subunit I (nadI) and internal transcribed spacer gene I (ITS1). After analysis of sequence information this was found that the fragment size of ITS1 of buffalo isolate was more in comparison to cattle and sheep isolates. Based on the nadI genotype this was found that Indian cattle, buffalo and sheep isolates could be grouped into E. granulosus sensu stricto. Based on coxI genotype two sheep isolates and one buffalo isolate were homologous to G2 genotype. Rests of the isolates were microvariants of G2 genotype. Presence of G2 genotype in buffalo is the first report of this genotype from this host.     

DNA polymorphism of insulin-like growth factor-binding protein-3 gene and its association with birth weight and body weight in cattle

Insulin‐like growth factor‐binding protein‐3 (IGFBP‐3) is a protein that binds the majority of insulin‐like growth factors in circulation for regulation of its action on growth and metabolism of the animals. Animals belonging to Hariana, Holstein‐Friesian (HF) and their crossbreds (HF × Hariana) were studied using polymerase chain reaction‐restriction fragment length polymorphism and nucleotide sequencing of the IGFBP‐3 gene. A 651‐bp fragment of the IGFBP‐3 gene spanning over a part of exon 2, complete intron 2, exon 3 and a part of intron 3 was amplified and digested with HaeIII restriction enzyme. Three patterns of restriction fragments were observed in HF and crossbred cattle revealing polymorphism in both the populations. The frequency of AA, AB and BB genotypes was 0.65, 0.32 and 0.03 in crossbreds and 0.29, 0.65 and 0.06 in HF respectively. The allelic frequency of the A and B allele was 0.81 and 0.19 in crossbreds and 0.62 and 0.38 in HF cattle respectively. Only one restriction pattern (AA genotype) was observed in all the animals of Hariana breed of Bos indicus showing the absence of polymorphism. Nucleotide sequencing revealed a C → A mutation in the intron 2 region of the IGFBP‐3 gene as the cause of the polymorphism. Least squares analysis revealed a significant effect (p < 0.05) of genotypes on birth weight and body weight (weight at 12, 18 and 24 months of age) of the animals. Animals of AB genotype showed higher birth weight and body weight than the animals possessing AA genotype.